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10 Amino Acids, Peptides, and Proteins

10 Amino Acids, Peptides, and Proteins

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23.10 AMINO ACIDS, PEPTIDES, AND PROTEINS



Nonpolar side chains



H2N



H



O



C



C



OH



H 2N



H



H



O



C



C



OH



H2N



CH3



Glycine (Gly)



H

H2N



C



Alanine (Ala)



O

C



H 2N



OH



C



C



OH



H2N



H



O



C



C



OH



CHCH2CH3



CH3



CH3



Valine (Val)



Isoleucine (Ile)

H

N



OH



C



C



O



CHCH3



O



H



H



H



O



C



C



H2N



C



C



OH



CH3

Leucine (Leu)



CH2



CH2CH2SCH3



O



CH2CHCH3



H2N



OH



H



H



O



C



C



OH



CH2

Proline (Pro)



Methionine (Met)



N

Phenylalanine (Phe)



H

Tryptophan (Trp)



Polar, neutral side chains



H2N



H



O



C



C



H



O



C



C



H2N



OH



CHCH3



CH2

OH



H



O



C



C



OH



CH2C



NH2



H2N



H



O



C



C



OH



C



C



H2N



CH2



H



O



C



C



OH



CH2

SH

Cysteine (Cys)



OH

Tyrosine (Tyr)

OH



CH2CH2C



O



NH2



O



Asparagine (Asn)



Glutamine (Gln)



Acidic side chains



H2N



O



OH

Threonine (Thr)



Serine (Ser)



H2N



H2N



OH



H



H



O



C



C



OH



CH2C



OH



O

Aspartic acid (Asp)



H2N



H



O



C



C



Basic side chains

H O

H2N



OH



CH2CH2C



C



C



H2N



OH



CH2CH2CH2CH2NH2



OH



H2N



O



C



C



OH



N

Histidine (His)

OH



Arginine (Arg)



Structures of the 20 ␣-amino acids found in proteins. Fifteen of the 20

have neutral side chains, two have acidic side chains, and three have basic

side chains. The names of the 9 essential amino acids are highlighted.



C



H



NH



CH2CH2CH2NHCNH2



Figure 23.8



C



N



O

H



O



CH2



Lysine (Lys)



Glutamic acid (Glu)



H



935



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Chapter 23 ORGANIC AND BIOLOGICAL CHEMISTRY



alpha- (A-) amino acids because the amine nitrogen atom in each is connected to the

carbon atom alpha to (next to) the carboxylic acid group. Nineteen of the 20 have an

¬ NH 2 amino group, and one (proline) has an ¬ NH ¬ amino group as part of a ring.

The 20 amino acids differ in the nature of the group attached to the A carbon.

Called the side chain, this group can be symbolized in a general way by the letter R.

Our bodies can synthesize only 11 of the 20 amino acids. The remaining 9, highlighted in Figure 23.8, are called essential amino acids because they must be obtained

from the diet.

α carbon



O

CH



R



᭡ Corn is particularly low in lysine, one

of the essential amino acids.



R



Generalized structure of

an α-amino acid



COH



NH2



Side chain



The 20 common amino acids are classified as neutral, basic, or acidic, depending

on the structure of their side chains. Fifteen of the 20 have neutral side chains. Two

(aspartic acid and glutamic acid) have an additional carboxylic acid group in their

side chains and are classified as acidic amino acids. Three (lysine, arginine, and histidine) have an additional amine function in their side chains and are classified as

basic amino acids. The 15 neutral amino acids can be further divided into those with

nonpolar side chains and those with polar functional groups such as amide or

hydroxyl groups. Nonpolar side chains are often described as hydrophobic (water

fearing) because they are not attracted to water, while polar side chains are described

as hydrophilic (water loving) because they are attracted to water.

Because amino acids can be assembled in any order, depending on which

¬ CO2H group forms an amide bond with which ¬ NH 2 group, the number of possible isomeric peptides increases rapidly as the number of amino acids increases.

There are six ways in which three different amino acids can be joined, more than

40,000 ways in which the eight amino acids present in the blood pressure-regulating

hormone angiotensin II can be joined (Figure 23.9), and a staggering number of ways

in which the 1800 amino acids in myosin, the major component of muscle filaments,

can be arranged.

No matter how long the chain, all noncyclic proteins have an N-terminal amino

acid with a free ¬ NH 2 on one end and a C-terminal amino acid with a free ¬ CO2H

on the other end. By convention, a protein is written with the free ¬ NH 2 on the left

and the free ¬ CO2H on the right, and its name is indicated using the three-letter

abbreviations listed in Figure 23.8.



Figure 23.9



The structure of angiotensin II, an

octapeptide present in blood plasma.



N terminal



H



C terminal



H



H



O



H



H



O



H



H



O



H



H



O



H



H



O



H



H



O



N



C



C



N



C



C



N



C



C



N



C



C



N



C



C



N



C



C



CH2



CH2



CHCH3



COOH



CH2



CH3



CH2



CHCH3



CH3



O



H



H



O



C



C



N



C



C



CH2



CH2



CH2



CH2



N



H



NH

N



OH



NH

C

HN

Asp



Arg



NH2

Val



Tyr



Ile



His



Pro



Phe



OH



23.11 CARBOHYDRATES

WORKED EXAMPLE 23.6



DRAWING A DIPEPTIDE STRUCTURE

Draw the structure of the dipeptide Ala-Ser.

STRATEGY



First, look up the names and structures of the two amino acids, Ala (alanine) and Ser

(serine). Since alanine is N-terminal and serine is C-terminal, Ala-Ser must have an

amide bond between the alanine ¬ CO2H and the serine ¬ NH 2.

SOLUTION

N terminal



O



H2NCHC



C terminal



O



NHCHCOH

CH2OH



CH3

Alanine



Serine

Ala-Ser



Ī PROBLEM 23.23 Which common amino acids contain an aromatic (benzene-like)

ring? Which contain sulfur? Which are alcohols? Which have alkyl-group side chains?

Ī PROBLEM 23.24 Use the three-letter shorthand notations to name the two isomeric

dipeptides that can be made from valine and cysteine. Draw both structures.

Ī PROBLEM 23.25



23.11



Name the six tripeptides that contain valine, tyrosine, and glycine.



CARBOHYDRATES



Carbohydrates occur in every living organism. The starch in food and the cellulose

in grass are nearly pure carbohydrate. Modified carbohydrates form part of the coating around all living cells, and other carbohydrates are found in the DNA that carries

genetic information from one generation to the next.

The word carbohydrate was used originally to describe glucose, which has the formula C6H 12O6 and was once thought to be a “hydrate of carbon,” C6(H 2O)6. This

view was soon abandoned, but the word persisted and is now used to refer to the

large class of hydroxyl-containing aldehydes and ketones that we commonly call

sugars. Glucose, for example, is a six-carbon aldehyde with five hydroxyl groups.



OH



O



HOCH2CHCHCHCHCH

HO OH



OH



Glucose—a pentahydroxy aldehyde



Carbohydrates are classified as either simple or complex. Simple sugars, or

monosaccharides, are carbohydrates such as glucose and fructose that can’t be

broken down into smaller molecules by hydrolysis with aqueous acid. Complex

carbohydrates, or polysaccharides, are compounds such as cellulose and starch that

are made of many simple sugars linked together and can be broken down by

hydrolysis.



937



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Chapter 23 ORGANIC AND BIOLOGICAL CHEMISTRY



Monosaccharides

Monosaccharides are further classified as either aldoses or ketoses. An aldose contains an aldehyde carbonyl group; a ketose contains a ketone carbonyl group (Section

23.8). The -ose suffix indicates a sugar, and the number of carbon atoms in the sugar

is specified by using the appropriate numerical prefix tri-, tetr-, pent-, or hex-. Thus,

glucose is an aldohexose (a six-carbon aldehyde sugar), fructose is a ketohexose

(a six-carbon ketone sugar), and ribose is an aldopentose (a five-carbon aldehyde

sugar). Most commonly occurring sugars are either aldopentoses or aldohexoses.

HO O



O



HOCH2CHCHCHCCH2OH



HOCH2CHCH



HO OH



HO OH



Fructose––a ketohexose



CHCH

OH



Ribose––an aldopentose



Glucose and other monosaccharides are often shown for convenience as having

open-chain structures. They actually exist, however, primarily as cyclic molecules in

which an ¬ OH group near one end of the chain adds to the carbonyl group at or

near the other end of the chain to form a ring. In glucose, ring formation occurs

between the ¬ OH group on C5 and the C “ O group at C1 (Figure 23.10).



H

HO



C



6



H

C



C



5



H



OH H



H

4



C



3



OH OH H



C



2



O

C



1



H



OH



Curl around

6



CH2OH



5



H

4



Form ring



OH



H



OH

H



OH

3



CH2OH



OH



H



OH

H



OH

α-Glucose



Form ring



H



2



OH

Open-chain glucose



H



H



OH



1



The α form has the –OH

group at C1 on the bottom side

of the ring.



The β form has the –OH

group on the top of the ring.



CH2OH



H

O



H



O



O



H

OH



H



OH



H



OH



H

H



OH

β-Glucose



Figure 23.10



The cyclic A and B forms of glucose.



Two cyclic forms of glucose can result from ring formation, depending on

whether the newly formed ¬ OH group at C1 is on the bottom or top side of the

ring. The ordinary crystalline glucose you might take from a bottle is entirely the

cyclic a form, in which the C1 ¬ OH group is on the bottom side of the ring. At equilibrium in water solution, however, all three forms are present in the proportion

0.02% open-chain form, 36% a form, and 64% b form.



Polysaccharides

Sucrose, or plain table sugar, is probably the most common pure organic chemical in

the world. Although sucrose is found in many plants, sugar beets (20% by mass) and

sugar cane (15% by mass) are the most common sources. Chemically, sucrose is a



23.12 LIPIDS



disaccharide composed of one molecule of glucose and one molecule of fructose

joined together. The 1 : 1 mixture of glucose and fructose that results from hydrolysis

of sucrose, often called invert sugar, is commonly used as a food additive.



6



CH2OH

5



4



1



CH2OH



O



1



O



OH

3



OH



OH



5



OH



3



2



OH



O



2



α-Glucose



4



CH2OH



6



β-Fructose



Sucrose



Cellulose, the fibrous substance that forms the structural material in grasses,

leaves, and stems, is a polysaccharide composed of several thousand b-glucose molecules joined together to form an immense chain.

CH2OH



CH2OH

CH2OH

O



OH



O



O



OH



O



O



OH



OH



O



Cellulose



OH

OH

β-Glucose units



Starch is also made of several thousand glucose units but, unlike cellulose, is

edible. Indeed, the starch in such vegetables as beans, rice, and potatoes is an essential part of the human diet. The two polysaccharides differ in that cellulose contains

b-glucose units while starch contains a-glucose units. Our stomachs contain

enzymes that are so specific in their action they are able to digest starch molecules

while leaving cellulose untouched.

Ī PROBLEM 23.26



Classify each of the following monosaccharides:



OH HO O



(a)



HOCH2CHCHCHCH

OH



23.12



(b)



O

HOCH2CCH2OH



(c)



OH



O



HOCH2CHCHCH

OH



LIPIDS



Lipids are less well-known to most people than proteins or carbohydrates, yet they

are just as essential to life. Lipids have many important biological functions, serving

as sources of fuel, as protective coatings around many plants and insects, and as

components of the membranes that enclose every living cell.

Chemically, a lipid is a naturally occurring organic molecule that dissolves in a

nonpolar organic solvent when a sample of plant or animal tissue is crushed or

ground. Because they’re defined by solubility, a physical property, rather than by



939



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Chapter 23 ORGANIC AND BIOLOGICAL CHEMISTRY



chemical structure, it’s not surprising that there are a great many different kinds of

lipids (Figure 23.11). Note that all the lipids in Figure 23.11 contain large hydrocarbon

portions, which accounts for their solubility behavior.

Figure 23.11



Structures of some

representative lipids. All are

isolated from plant and animal

tissue by extraction with

nonpolar organic solvents, and

all have large hydrocarbon

portions.



Fatty acid



O

CH2OCCH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

O

CHOCCH2CH2CH2CH2CH2CH2CH2CH



CHCH2CH2CH2CH2CH2CH2CH2CH3



O

CH2OCCH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

A triglyceride (animal fat or vegetable oil)



CH3



OH

CO2H



CH3

OH

HO

Cholesterol––a steroid



OH

PGF2α––a prostaglandin



Animal fats and vegetable oils are the most abundant lipids in nature. Although

they appear physically different—animal fats like butter and lard are usually solid

while vegetable oils like corn and peanut oil are liquid—their structures are similar. All

fats and oils are triacylglycerols, or triglycerides—esters of glycerol (1,2,3-propanetriol)

with three long-chain carboxylic acids called fatty acids. The fatty acids are usually

straight-chain rather than branched and have an even number of carbon atoms in the

range 12–22. If they are unsaturated, their double bonds are usually cis rather than

trans. Table 23.3 gives the structures of some commonly occurring fatty acids.

TABLE 23.3



Structures of Some Common Fatty Acids



Name



No. of

Carbons



No. of

Double

Bonds



Saturated

Myristic

Palmitic

Stearic



14

16

18



0

0

0



CH 3(CH 2)12CO2H

CH 3(CH 2)14CO2H

CH 3(CH 2)16CO2H



Unsaturated

Oleic

Linoleic



18

18



1

2



Linolenic



18



3



CH 3(CH 2)7CH “ CH(CH 2)7CO2H (cis)

CH 3(CH 2)4CH “ CHCH 2CH “ CH(CH 2)7CO2H (all cis)

CH 3CH 2CH “ CHCH 2CH “ CHCH 2CH “ CH(CH 2)7CO2H (all cis)



Structure



As shown by the triacylglycerol structure in Figure 23.11, the three fatty acids of a

given molecule need not be the same. Furthermore, the fat or oil from a given source

is a complex mixture of many different triacylglycerols.



23.13 NUCLEIC ACIDS



About 40 different fatty acids occur naturally. Palmitic acid (C16) and stearic

acid (C18) are the most abundant saturated acids; oleic and linoleic acids (both C18)

are the most abundant unsaturated ones. Oleic acid is monounsaturated because it

has only one double bond, but linoleic and linolenic acids are polyunsaturated fatty

acids because they have more than one carbon–carbon double bond. For reasons

that are not yet clear, a diet rich in saturated fats leads to a higher level of blood

cholesterol and consequent higher risk of heart attack than a diet rich in unsaturated fats.

The main difference between animal fats and vegetable oils is that vegetable

oils generally have a higher proportion of unsaturated fatty acids than do animal

fats. The double bonds in vegetable oils can be hydrogenated to yield saturated fats

in the same way that any alkene can react with hydrogen to yield an alkane

(Section 23.4). By carefully controlling the extent of hydrogenation, the final product can have any desired consistency. Margarine, for example, is prepared so that

only about two-thirds of the double bonds present in the starting vegetable oil are

hydrogenated.

Ī PROBLEM 23.27 Show the structure of glyceryl trioleate, a fat molecule whose components are glycerol and three oleic acid units.



23.13



NUCLEIC ACIDS



How does a seed “know” what kind of plant to become? How does a fertilized ovum

know how to grow into a human being? How does a cell know what part of the body

it’s in? The answers to such questions involve the biological molecules called nucleic

acids.

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the chemical carriers of an organism’s genetic information. Coded in an organism’s DNA is all the

information that determines the nature of the organism and all the directions that are

needed for producing the many thousands of different proteins required by the

organism.

Just as proteins are made of amino acid units linked together, nucleic acids

are made of nucleotide units linked together in a long chain. Each nucleotide is

composed of a nucleoside plus phosphoric acid, H 3PO4, and each nucleoside is composed of an aldopentose sugar plus an amine base.

Phosphate

Sugar



Sugar

H3PO4



+

Amine base



Many



Sugar



Nucleic acid



nucleotides

Amine base

Amine base



Nucleoside



Nucleotide



The sugar component in RNA is ribose, and the sugar in DNA is 2-deoxyribose,

where “2-deoxy” means that oxygen is missing from C2 of ribose.

5



HOCH2

4



OH



O



1



3



2



OH



OH



Ribose



5



HOCH2

4



OH



O



3



1

2



OH

2-Deoxyribose



941



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Chapter 23 ORGANIC AND BIOLOGICAL CHEMISTRY



Four different cyclic amine bases occur in DNA: adenine, guanine, cytosine, and

thymine. Adenine, guanine, and cytosine also occur in RNA, but thymine is replaced

in RNA by a related base called uracil.

NH2

N

N



N

N



H



NH2



O

N

N



H



N

N



NH2



Guanine (G)

DNA

RNA



N



O



H3C



N



H



Adenine (A)

DNA

RNA



O

H



N



O



N



O



N



N



H



H



H



Cytosine (C)

DNA

RNA



Thymine (T)

DNA



Uracil (U)

RNA



H

O



In both DNA and RNA, the cyclic amine base is bonded to C1’ of the sugar, and

the phosphoric acid is bonded to the C5’ sugar position. Thus, nucleosides and

nucleotides have the general structures shown in Figure 23.12. (Numbers with a prime

superscript refer to positions on the sugar component of a nucleotide, and numbers

without a prime refer to positions on the cyclic amine base.)

Figure 23.12



General structures of (a) a nucleoside

and (b) a nucleotide.



(a) A nucleoside



(b) A nucleotide



Amine

base

HO



CH2



Phosphate



O



O

−O



N



P



O



CH2



O



N



Amine

base



O−

OH



Y



OH



Y



Sugar



Sugar



When Y = H, the sugar is deoxyribose;

when Y = OH, the sugar is ribose.



Nucleotides join together in nucleic acids by forming a bond between the phosphate group at the 5’ position of one nucleotide and the hydroxyl group on the sugar

component at the 3’ position of another nucleotide (Figure 23.13).



5′ end



Phosphate



Sugar



Base



Phosphate



Sugar



O



P



O−



O



CH2



3′ position

Base



Base



O



O

O



P



O−



O



CH2



5′ position



Phosphate



O

3′ end



Figure 23.13



Generalized structure of a nucleic acid.



Sugar



Base



O



Base



23.13 NUCLEIC ACIDS



Just as the structure of a protein depends on the sequence of its individual amino

acids, the structure of a nucleic acid depends on the sequence of its individual

nucleotides. That sequence is described by starting at the 5’ phosphate end of the

chain and identifying the bases in order. Abbreviations are used for each nucleotide:

A for adenosine, G for guanosine, C for cytidine, T for thymidine, and U for uracil.

Thus, a portion of a DNA sequence might be written -T-A-G-G-C-T-.

Interestingly, molecules of DNA isolated from different tissues of the same

species have the same proportions of nucleotides, but molecules from different

species can have quite different proportions. For example, human DNA contains

about 30% each of A and T and about 20% each of G and C, whereas the bacterium Clostridium perfringens contains about 37% each of A and T and only 13%

each of G and C. Note that in both cases, the bases occur in pairs. Adenine and

thymine are usually present in equal amounts, as are guanine and cytosine. Why

should this be?

According to the Watson–Crick model, DNA consists of two polynucleotide

strands coiled around each other in a double helix like the handrails on a spiral staircase. The sugar–phosphate backbone is on the outside of the helix, and the amine

bases are on the inside, so that a base on one strand points directly in toward a base

on the second strand. The two strands run in opposite directions and are held

together by hydrogen bonds between pairs of bases. Adenine and thymine form two

strong hydrogen bonds to each other, but not to G or C; G and C form three strong

hydrogen bonds to each other, but not to A or T (Figure 23.14).



Electrostatic potential maps show that the faces of the

bases are relatively neutral (green), while the edges

have positive (blue) and negative (red) regions.



H

N



N

N



N



H

H



O



CH3



N



N



N

O



A



T



H

O



N

N



H



N



N



H



N



N



H



O



N



N

H



G



C

Pairing A with T and G with C brings

together oppositely charged regions.



Figure 23.14



Hydrogen bonding between base pairs in the DNA double helix.



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Chapter 23 ORGANIC AND BIOLOGICAL CHEMISTRY



The two strands of the DNA double helix aren’t identical; rather, they’re complementary. Whenever a G base occurs in one strand, a C base occurs opposite it in the

other strand because of hydrogen bonding. When an A base occurs in one strand, a T

base occurs in the other strand. This complementary pairing of bases explains why A

and T are always found in equal amounts, as are G and C. Figure 23.15 shows how the

two complementary strands coil into the double helix.

The DNA of higher organisms, both plant and animal, is found primarily in the

nucleus of cells in the form of threadlike strands that are coated with proteins and

wound into complex assemblies called chromosomes. Each chromosome is made up of

several thousand genes, where a gene is a segment of a DNA chain that contains the

instructions necessary to make a specific protein. By decoding the right genes at the

right time, an organism uses genetic information to synthesize the thousands of proteins needed for living. DNA thus acts as the storage medium for an organism’s

genetic information, which RNA then reads, decodes, and uses to make proteins.

Three main processes take place in the transfer and use of genetic information.

Replication is the process by which identical copies of DNA are made, forming additional molecules and preserving genetic information for passing on to offspring.

Transcription is the process by which information in the DNA is transferred to and

decoded by RNA. Translation is the process by which RNA uses the information to

build proteins.

Figure 23.15



The DNA double helix. The coil of the

sugar–phosphate backbone is visible on

the outside of the DNA double helix,

while the hydrogen-bonded pairs of

amine bases lie flat on the inside.



Replication

DNA replication begins with a partial unwinding of the double helix. As the DNA

strands separate and bases are exposed, new nucleotides line up on each strand in a

complementary manner, A to T and C to G, and two new strands begin to grow. Each

new strand is complementary to its old template strand, so two new, identical DNA

double helixes are produced (Figure 23.16).



5′ New



1. A portion of the DNA

double helix unwinds.

3′ Old



3′ Old

2. Complementary nucleotides

line up for linking to yield

two new DNA molecules.



3. Each of the new DNA molecules

contains one of the original

strands and one new strand.



5′ Old

A

T

G

C



Figure 23.16



5′ Old



3′ New



DNA replication.



Transcription

The genetic instructions contained in DNA are transcribed into RNA when a small

portion of the DNA double helix unwinds and one of the two DNA strands acts as

a template for complementary ribonucleotides to line up, a process similar to that

of DNA replication (Figure 23.17). The only difference is that uracil (U) rather



23.13 NUCLEIC ACIDS



945



Figure 23.17



Transcription of DNA to synthesize

RNA.



1. A small portion of the DNA

double helix unwinds.



DNA



DNA template strand

2. One of the two DNA

strands acts as a

template on which

ribonucleotides line up.

Complementary

mRNA strand

3. The RNA produced is complementary

to the DNA strand from which it is

transcribed.



than thymine lines up opposite adenine. Once completed, the RNA molecule separates from the DNA template, and the DNA rewinds to its stable double-helix

conformation.



Translation

Protein biosynthesis is directed by a special kind of RNA called messenger RNA, or

mRNA, and takes place on knobby protuberances within a cell called ribosomes. The

specific ribonucleotide sequence in mRNA acts like a long series of words that spell

out how proteins are to be constructed.

Each “word” along the mRNA chain consists of a series of three ribonucleotides

that is specific for a given amino acid. For example, the series cytosine–uracil–

guanine (C-U-G) on mRNA is a three-letter word directing that the amino acid

leucine be incorporated into the growing protein. The words are read by another

kind of RNA called transfer RNA, or tRNA. Each of the 60 or so different tRNAs

contains a complementary base sequence that allows it to recognize a three-letter

word on mRNA and act as a carrier to bring a specific amino acid into place for

transfer to the growing peptide chain (Figure 23.18). When synthesis of the protein

is complete, a “stop” word signals the end and the protein is released from the

ribosome.



1. Messenger RNA is read by tRNA

that contains complementary threebase sequences.

Messenger RNA chain

Transfer RNAs

lining up with

amino acids

AA1



AA2



AA3



Growing peptide chain

2. Transfer RNA then assembles the

proper amino acids (AA1, AA2, and

so on) into position for incorporation

into the peptide.



AA4



AA5



Figure 23.18



Protein biosynthesis.



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